(a) Workflow for the PheWAS analysis. D2 genome was sequenced using Illumina and SOLiD platforms and aligned to the reference genome. Approximately five million sequence and structural variants were identified. A set of high-impact variants including 11,979 missense, 58 nonsense, 70 splice site, 45 frame shift and 276 CNVs spanning at least one gene was used for classic and molecular PheWAS analyses. (b) Whole-genome read coverage. The distribution was generated using combined mapped reads from Illumina and SOLiD, and mapped reads from Illumina and SOLiD platforms individually. (c) Circos plot of sequence and structure variants segregating in the BXD cohort. The outmost circle represents SNP density per 100 kb window (black at the lowest density and orange at the highest density). The second circle represents indel density per 100 kb. The innermost circle represents CNVs. Blue and green ticks indicate D2 losses and gains, respectively. (d) Venn diagram of missense variants predicted to be deleterious by SIFT and PolyPhen2. (e) False positive rate of strong variants. A small subset of each type of variants was selected for validation by Sanger resequencing.